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<h1>
<a href="index.html">AQUA</a></h1>

<address>
Jurgen Doreleijers, Madison, <a href="mailto:jurgenfd@gmail.com">jurgenfd@gmail.com</a></address>

<address>
Ton Rullmann, Utrecht</address>

<br>&nbsp;</td>

<td>
<blockquote>
<div align=right><img SRC="aqua.gif" height=108 width=108 align=RIGHT></div>
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<h2>

<hr WIDTH="100%"></h2>

<h2>
HOW_TO_USE</h2>

<h2>
Contents</h2>

<ol>
<li>
<a href="#1. INITIALIZATION">INITIALIZATION</a></li>

<li>
<a href="#2. USING AQUA - COMMAND OVERVIEW">USING AQUA - COMMAND OVERVIEW</a></li>

<li>
<a href="#3. FURTHER INFORMATION">FURTHER INFORMATION</a></li>
</ol>

<h2>

<hr WIDTH="100%"></h2>

<h2>
<a NAME="1. INITIALIZATION"></a>1. Initialization</h2>
Before using Aqua, either interactively or from within a script, you have
to initialize a serious of variables and aliases.
<p>Define the directory root (if the system manager has not already done
so) and call (substituting X.Y with the current version number):
<pre>&nbsp;&nbsp;&nbsp; setenv aquaroot $YOUR_LOCATION/aquaX.Y</pre>
Prepare for interactive use with:
<pre>&nbsp;&nbsp;&nbsp; source $aquaroot/aqsetupi</pre>
Prepare for use in a script with:
<pre>&nbsp;&nbsp;&nbsp; source $aquaroot/aqsetup</pre>
Alternatively, you may want to store the equivalent definition in your
'.cshrc' file (if the system manager has not already provided definitions).
An alias for initializing the Aqua setup may also be defined there:
<pre>&nbsp;&nbsp;&nbsp; setenv aquaroot $YOUR_LOCATION/aquaX.Y
&nbsp;&nbsp;&nbsp; alias aqua 'source $aquaroot/aqsetupi'</pre>

<p><br>Then, before running AQUA you can initialize the program simply
by typing:
<pre>&nbsp;&nbsp;&nbsp; aqua</pre>
I advise you not to import definitions from the 'aqsetup' script into places
like '.cshrc'.
<p>
<hr WIDTH="100%">
<h2>
<a NAME="2. USING AQUA - COMMAND OVERVIEW"></a>2. Using AQUA - command
overview</h2>

<p><br>This file gives a short overview of the commands.
<p><i>NOTE: NOT ALL PROGRAM OPTIONS ARE DISCUSSED HERE.</i>
<p>For more detailed information you may
<ul>
<li>
consult the on-line <a href="http://www.nmr.chem.uu.nl/users/rull/pcheck_dir/nmr_manual/">manual</a>
(somewhat outdated)</li>

<li>
use the 'qhelp' command (more topics than currently in on-line manual)</li>

<li>
read the files in $AQUADOCDIR (equivalent of using 'qhelp').</li>
</ul>
Running Aqua consists of three steps:
<ol>
<li>
&nbsp;1. Convert restraints to Aqua format: command 'qconvert', see 2.2.</li>

<li>
&nbsp;2. Analyze restraint violations: command 'aqpc', see 2.3.</li>

<li>
&nbsp;3. Inspect results, either interactively (commands 'qsumm', 'qdbext'
and 'qanal'; see 2.4) or via Procheck-NMR (see 2.5).</li>
</ol>
Remarks on notation:
<ul>
<li>
square brackets [] indicate an optional command switch (presence not required)</li>

<li>
the order of the options is irrelevant, unless indicated otherwise</li>

<li>
CAPITAL letters indicate a position where you have to substitute the name
of a file (or part of a name)</li>
</ul>

<h4>
2.1 HELP INFORMATION</h4>

<pre>&nbsp;&nbsp;&nbsp; qhelp [options]</pre>
The qhelp command lists information about commands, file formats and implementation
issues. Typing 'qhelp' without additional options lists the available topics.
<h4>
2.2. CONVERT RESTRAINT FILE</h4>
See 'qhelp qconvert' for a description of the progam, details and command
options.
<h4>
2.3. COMPUTE RESTRAINT VIOLATIONS</h4>
See 'qhelp qconvert' for a description of the progam, details and command
options.
<h4>
2.4. INSPECT VIOLATIONS</h4>
The root names of the output files produced by AQUA are defined by the
current project name, cf. previous paragraph.
<br>The names of the output files have the following extensions, each indicating
the type of data the file contains:
<pre>&nbsp;&nbsp;&nbsp; summary:&nbsp;&nbsp;&nbsp;&nbsp; .nsm (noe),&nbsp; .hsm (hb),&nbsp; .ssm (ss),&nbsp; .dsm (dis)
&nbsp;&nbsp;&nbsp; violations:&nbsp; .nrv (noe),&nbsp; .hrv (hb),&nbsp; .srv (ss),&nbsp; .drv (dis)
&nbsp;&nbsp;&nbsp; counts:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; .nrc (noe),&nbsp; .hrc (hb),&nbsp; .src (ss),&nbsp; .drc (dis)</pre>
where
<ul>
<li>
&nbsp;&nbsp;&nbsp;&nbsp; (noe) refer to the NOE distance restraints</li>

<li>
&nbsp;&nbsp;&nbsp;&nbsp; (hb)&nbsp; refer to the Hydrogen bond distance
restraints</li>

<li>
&nbsp;&nbsp;&nbsp;&nbsp; (ss)&nbsp; refer to the disulphide distance restraints</li>

<li>
&nbsp;&nbsp;&nbsp;&nbsp; (dis) refer to the generic distance restraints</li>
</ul>
These files are ASCII text files and can be printed out or read with any
text editor.
<p>The script 'qdbext' can be used to extract data from the '.?rv' (violations)&nbsp;
and '.?rc' (counts) files on a keyword basis; see 'qhelp qdbext' and&nbsp;
'qhelp dbas'.
<p>Additionally, you can generate a new summary file using the 'qsumm'
script. This gives a longer list of largest violations (by default only
the largest three are shown for each structure). To do this, give the command:
<pre>&nbsp;&nbsp;&nbsp; qsumm&nbsp; VIOLATIONS_FILE&nbsp; COUNTS_FILE&nbsp; [MAX_LINES] [ > OUTPUT_FILE]</pre>
Also see 'qhelp qsumm'.
<p>Another script for summarizing the results of Aqua calculations is 'qanal',
written by Kris Boulez. This script can only be used if Perl5 is installed
on your computer. See 'qhelp qanal'.
<h4>
2.5. VISUALIZE DISTANCE AND ANGLE RESTRAINT VIOLATIONS WITH PROCHECK-NMR</h4>
See 'qhelp procheck' for more details.
<p>
<hr WIDTH="100%">
<h2>
<a NAME="3. FURTHER INFORMATION"></a>3. Further information</h2>
Besides the programs and scripts mentioned above, information on various
topics is available through the 'qhelp' command. Type 'qhelp' to get a
list of commands and topics.
<br>
<hr>
<p>Contact the <a href="mailto:jurgenfd@gmail.com">author</a> or <a href="mailto:webmaster@bmrb.wisc.edu">webmaster</a>
for help, when required.
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